library(tidyverse)
library(tidylog)
library(brms)
library(tidybayes)
library(modelr)
library(viridis)
library(purrr)
library(ggsidekick)
theme_set(theme_sleek())
# For parallel processing
options(mc.cores = parallel::detectCores())
# Continuous colors
options(ggplot2.continuous.colour = "viridis")
# Discrete colors
scale_colour_discrete <- function(...) {
scale_colour_brewer(palette = "Paired")
}
scale_fill_discrete <- function(...) {
scale_fill_brewer(palette = "Paired")
}
d <- readr::read_csv("data/for_analysis/dat.csv") %>%
select(-...1) %>%
mutate(length_cm = length_mm / 10)
# qwraps2::lazyload_cache_dir(path = "R/03b_preliminary_analysis_cache/html")
ggplot(d, aes(age_bc, length_cm, color = cohort)) +
geom_point(size = 1/2, alpha = 1/4) +
facet_wrap(~area)
# Filter cohorts with minimum 5 IDs per cohort
d <- d %>%
group_by(cohort, area) %>%
mutate(n_id = length(unique(ID))) %>%
filter(n_id >= 10) %>%
ungroup()
#> group_by: 2 grouping variables (cohort, area)
#> mutate (grouped): new variable 'n_id' (integer) with 298 unique values and 0% NA
#> filter (grouped): removed 1,404 rows (<1%), 363,142 rows remaining
#> ungroup: no grouping variables
brms models for each cohort with
parameters varying among individuals for each areaFirst run some prior predictive checks to make sure priors are reasonable
hist(rnorm(100000, mean = 40, sd = 20))
hist(rnorm(100000, mean = -0.5, sd = 1))
hist(rnorm(100000, mean = 0.2, sd = 1))
m0 <- brm(
bf(length_cm ~ Linf*(1-exp(-K*(age_bc-t0))),
Linf ~ 1, t0 ~ 1, K ~ 1, nl = TRUE),
data = d, family = gaussian(),
prior = c(prior(normal(45, 20), nlpar = "Linf"),
prior(normal(-0.5, 1), nlpar = "t0"),
prior(normal(0.2, 0.1), nlpar = "K")),
sample_prior = "only",
iter = 4000, thin = 1, cores = 3, chains = 3, seed = 9)
#> Compiling Stan program...
#> Start sampling
pp <- conditional_effects(m0, method = "posterior_predict")
plot(pp, plot = FALSE)[[1]] +
labs(x = "Age [yrs]", y = "length [cm]") +
geom_point(data = d, aes(age_bc, length_cm), inherit.aes = FALSE)
#
# # Global model
# p1 <- ggplot(d, aes(age_bc, length_cm)) +
# geom_jitter(height = 0, width = 0.5, alpha = 0.2, shape = 21, fill = "black", color = "white") +
# coord_cartesian(expand = 0, ylim = c(0, 55), xlim = c(0, 18))
# Sub sample for faster fitting...
# d_sub <- sample_n(d, 5000)
#
# p2 <- ggplot(d_sub, aes(age_bc, length_cm)) +
# geom_jitter(height = 0, width = 0.5, alpha = 0.2, shape = 21, fill = "black", color = "white") +
# coord_cartesian(expand = 0, ylim = c(0, 55), xlim = c(0, 18))
#
# p1 / p2
#
# m1 <- brm(
# bf(length_cm ~ Linf*(1-exp(-K*(age_bc-t0))),
# Linf ~ 1, t0 ~ 1, K ~ 1, nl = TRUE),
# data = d_sub, family = student(),
# prior = c(prior(normal(40, 20), nlpar = "Linf"),
# prior(normal(-0.5, 0.5), nlpar = "t0"),
# prior(normal(0.2, 0.1), nlpar = "K")),
# iter = 3000, thin = 1, cores = 3, chains = 3)
#
# summary(m1)
#
# rhat(m1)
#
# plot(m1)
#
# pp <- conditional_effects(m1, method = "posterior_predict")
#
# plot(pp, plot = FALSE)[[1]] +
# labs(x = "Age [yrs]", y = "length [cm]") +
# geom_point(data = d_sub, aes(age_bc, length_cm), inherit.aes = FALSE)
Test a cohort-specific vbge model to the area with least years to start with
d %>%
group_by(area) %>%
summarise(n_cohorts = length(unique(cohort))) %>%
arrange(n_cohorts)
#> group_by: one grouping variable (area)
#> summarise: now 12 rows and 2 columns, ungrouped
d_vin <- d %>% filter(area == "VN")
#> filter: removed 352,404 rows (97%), 10,738 rows remaining
# Plot VN area
ggplot(d_vin, aes(age_bc, length_cm, color = ID)) +
geom_point(size = 1/2, alpha = 1/4) +
facet_wrap(~cohort) +
guides(color = "none") +
scale_color_viridis(discrete = TRUE)
# Fit model with parameters varying by ID. First filter a single year to test speed
start_time <- Sys.time()
mtest <-
brm(
bf(length_cm ~ Linf*(1-exp(-K*(age_bc-t0))),
t0 ~ 1 + (1|ID),
K ~ 1 + (1|ID),
Linf ~ 1 + (1|ID),
nl = TRUE),
data = filter(d_vin, cohort == 1995),
family = gaussian(),
prior = c(prior(normal(45, 20), nlpar = "Linf"),
prior(normal(0.5, 1), nlpar = "t0"),
prior(normal(0.2, 0.1), nlpar = "K")),
iter = 4000,
thin = 1,
cores = 3,
chains = 3,
seed = 9)
#> filter: removed 9,800 rows (91%), 938 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
Sys.time() - start_time
#> Time difference of 8.641417 mins
rhat(mtest)
#> b_t0_Intercept b_K_Intercept
#> 1.0001327 1.0002526
#> b_Linf_Intercept sd_ID__t0_Intercept
#> 1.0001181 1.0007497
#> sd_ID__K_Intercept sd_ID__Linf_Intercept
#> 1.0148756 1.0007793
#> sigma r_ID__t0[1996_246_VN,Intercept]
#> 1.0005787 0.9999792
#> r_ID__t0[1997_102_VN,Intercept] r_ID__t0[1997_105_VN,Intercept]
#> 1.0000238 1.0000997
#> r_ID__t0[1997_106_VN,Intercept] r_ID__t0[1997_107_VN,Intercept]
#> 0.9997177 0.9997777
#> r_ID__t0[1997_108_VN,Intercept] r_ID__t0[1997_109_VN,Intercept]
#> 0.9996247 0.9996072
#> r_ID__t0[1997_11_VN,Intercept] r_ID__t0[1997_110_VN,Intercept]
#> 0.9998074 1.0006909
#> r_ID__t0[1997_113_VN,Intercept] r_ID__t0[1997_115_VN,Intercept]
#> 0.9998463 0.9996394
#> r_ID__t0[1997_12_VN,Intercept] r_ID__t0[1997_13_VN,Intercept]
#> 0.9998311 0.9996200
#> r_ID__t0[1997_14_VN,Intercept] r_ID__t0[1997_15_VN,Intercept]
#> 0.9998524 1.0002598
#> r_ID__t0[1997_151_VN,Intercept] r_ID__t0[1997_152_VN,Intercept]
#> 1.0001044 0.9998308
#> r_ID__t0[1997_153_VN,Intercept] r_ID__t0[1997_156_VN,Intercept]
#> 1.0000606 0.9998750
#> r_ID__t0[1997_157_VN,Intercept] r_ID__t0[1997_159_VN,Intercept]
#> 1.0001748 0.9998840
#> r_ID__t0[1997_160_VN,Intercept] r_ID__t0[1997_162_VN,Intercept]
#> 0.9995350 0.9997479
#> r_ID__t0[1997_17_VN,Intercept] r_ID__t0[1997_18_VN,Intercept]
#> 0.9997359 0.9995329
#> r_ID__t0[1997_189_VN,Intercept] r_ID__t0[1997_19_VN,Intercept]
#> 1.0001025 0.9998749
#> r_ID__t0[1997_190_VN,Intercept] r_ID__t0[1997_192_VN,Intercept]
#> 0.9997635 0.9999726
#> r_ID__t0[1997_193_VN,Intercept] r_ID__t0[1997_195_VN,Intercept]
#> 1.0002050 0.9999054
#> r_ID__t0[1997_199_VN,Intercept] r_ID__t0[1997_20_VN,Intercept]
#> 0.9998029 0.9997970
#> r_ID__t0[1997_201_VN,Intercept] r_ID__t0[1997_21_VN,Intercept]
#> 0.9997989 1.0001056
#> r_ID__t0[1997_211_VN,Intercept] r_ID__t0[1997_212_VN,Intercept]
#> 0.9998184 0.9997609
#> r_ID__t0[1997_213_VN,Intercept] r_ID__t0[1997_217_VN,Intercept]
#> 1.0003063 0.9997863
#> r_ID__t0[1997_218_VN,Intercept] r_ID__t0[1997_219_VN,Intercept]
#> 0.9999291 1.0002079
#> r_ID__t0[1997_220_VN,Intercept] r_ID__t0[1997_222_VN,Intercept]
#> 1.0005136 0.9998404
#> r_ID__t0[1997_223_VN,Intercept] r_ID__t0[1997_226_VN,Intercept]
#> 1.0003571 0.9997255
#> r_ID__t0[1997_227_VN,Intercept] r_ID__t0[1997_229_VN,Intercept]
#> 0.9997597 1.0006333
#> r_ID__t0[1997_23_VN,Intercept] r_ID__t0[1997_230_VN,Intercept]
#> 0.9997934 0.9997155
#> r_ID__t0[1997_235_VN,Intercept] r_ID__t0[1997_236_VN,Intercept]
#> 0.9999956 0.9996559
#> r_ID__t0[1997_240_VN,Intercept] r_ID__t0[1997_241_VN,Intercept]
#> 1.0002541 0.9998921
#> r_ID__t0[1997_244_VN,Intercept] r_ID__t0[1997_248_VN,Intercept]
#> 0.9996930 0.9999447
#> r_ID__t0[1997_250_VN,Intercept] r_ID__t0[1997_252_VN,Intercept]
#> 0.9998795 0.9996383
#> r_ID__t0[1997_253_VN,Intercept] r_ID__t0[1997_254_VN,Intercept]
#> 0.9999164 0.9995759
#> r_ID__t0[1997_256_VN,Intercept] r_ID__t0[1997_257_VN,Intercept]
#> 0.9996287 0.9997100
#> r_ID__t0[1997_258_VN,Intercept] r_ID__t0[1997_263_VN,Intercept]
#> 0.9997546 0.9997915
#> r_ID__t0[1997_268_VN,Intercept] r_ID__t0[1997_270_VN,Intercept]
#> 0.9999677 0.9998390
#> r_ID__t0[1997_271_VN,Intercept] r_ID__t0[1998_102_VN,Intercept]
#> 1.0001919 1.0001179
#> r_ID__t0[1998_103_VN,Intercept] r_ID__t0[1998_11_VN,Intercept]
#> 1.0002532 0.9995579
#> r_ID__t0[1998_110_VN,Intercept] r_ID__t0[1998_111_VN,Intercept]
#> 1.0001786 0.9998030
#> r_ID__t0[1998_12_VN,Intercept] r_ID__t0[1998_121_VN,Intercept]
#> 0.9999119 0.9995252
#> r_ID__t0[1998_122_VN,Intercept] r_ID__t0[1998_123_VN,Intercept]
#> 1.0004306 0.9998765
#> r_ID__t0[1998_124_VN,Intercept] r_ID__t0[1998_125_VN,Intercept]
#> 0.9997801 0.9999055
#> r_ID__t0[1998_127_VN,Intercept] r_ID__t0[1998_128_VN,Intercept]
#> 1.0004825 0.9995907
#> r_ID__t0[1998_129_VN,Intercept] r_ID__t0[1998_13_VN,Intercept]
#> 0.9999933 0.9998804
#> r_ID__t0[1998_138_VN,Intercept] r_ID__t0[1998_14_VN,Intercept]
#> 0.9995762 1.0005225
#> r_ID__t0[1998_140_VN,Intercept] r_ID__t0[1998_143_VN,Intercept]
#> 0.9997871 0.9996229
#> r_ID__t0[1998_145_VN,Intercept] r_ID__t0[1998_146_VN,Intercept]
#> 1.0000988 0.9995714
#> r_ID__t0[1998_148_VN,Intercept] r_ID__t0[1998_149_VN,Intercept]
#> 0.9998828 1.0007830
#> r_ID__t0[1998_155_VN,Intercept] r_ID__t0[1998_17_VN,Intercept]
#> 0.9998128 1.0003273
#> r_ID__t0[1998_273_VN,Intercept] r_ID__t0[1998_285_VN,Intercept]
#> 0.9999381 1.0000081
#> r_ID__t0[1998_288_VN,Intercept] r_ID__t0[1998_289_VN,Intercept]
#> 1.0002351 0.9998218
#> r_ID__t0[1998_29_VN,Intercept] r_ID__t0[1998_290_VN,Intercept]
#> 0.9996038 0.9995739
#> r_ID__t0[1998_291_VN,Intercept] r_ID__t0[1998_292_VN,Intercept]
#> 0.9995544 0.9996374
#> r_ID__t0[1998_295_VN,Intercept] r_ID__t0[1998_3_VN,Intercept]
#> 0.9999513 0.9997984
#> r_ID__t0[1998_30_VN,Intercept] r_ID__t0[1998_303_VN,Intercept]
#> 0.9995570 0.9996685
#> r_ID__t0[1998_304_VN,Intercept] r_ID__t0[1998_305_VN,Intercept]
#> 0.9996181 1.0001049
#> r_ID__t0[1998_306_VN,Intercept] r_ID__t0[1998_31_VN,Intercept]
#> 1.0001960 1.0000714
#> r_ID__t0[1998_315_VN,Intercept] r_ID__t0[1998_32_VN,Intercept]
#> 0.9998489 0.9998505
#> r_ID__t0[1998_323_VN,Intercept] r_ID__t0[1998_327_VN,Intercept]
#> 1.0000816 1.0004230
#> r_ID__t0[1998_329_VN,Intercept] r_ID__t0[1998_33_VN,Intercept]
#> 0.9998894 1.0002768
#> r_ID__t0[1998_330_VN,Intercept] r_ID__t0[1998_332_VN,Intercept]
#> 1.0015513 1.0002537
#> r_ID__t0[1998_333_VN,Intercept] r_ID__t0[1998_334_VN,Intercept]
#> 1.0000826 0.9995901
#> r_ID__t0[1998_335_VN,Intercept] r_ID__t0[1998_336_VN,Intercept]
#> 1.0000267 0.9997047
#> r_ID__t0[1998_337_VN,Intercept] r_ID__t0[1998_338_VN,Intercept]
#> 1.0001809 1.0000923
#> r_ID__t0[1998_339_VN,Intercept] r_ID__t0[1998_34_VN,Intercept]
#> 0.9999423 0.9997508
#> r_ID__t0[1998_340_VN,Intercept] r_ID__t0[1998_341_VN,Intercept]
#> 0.9998269 1.0003535
#> r_ID__t0[1998_342_VN,Intercept] r_ID__t0[1998_343_VN,Intercept]
#> 0.9997683 0.9998582
#> r_ID__t0[1998_349_VN,Intercept] r_ID__t0[1998_35_VN,Intercept]
#> 0.9999369 0.9997555
#> r_ID__t0[1998_352_VN,Intercept] r_ID__t0[1998_36_VN,Intercept]
#> 1.0001368 1.0005061
#> r_ID__t0[1998_37_VN,Intercept] r_ID__t0[1998_397_VN,Intercept]
#> 1.0005753 0.9996383
#> r_ID__t0[1998_4_VN,Intercept] r_ID__t0[1998_400_VN,Intercept]
#> 0.9997917 0.9995447
#> r_ID__t0[1998_401_VN,Intercept] r_ID__t0[1998_402_VN,Intercept]
#> 1.0001376 0.9996565
#> r_ID__t0[1998_407_VN,Intercept] r_ID__t0[1998_45_VN,Intercept]
#> 0.9996432 0.9996745
#> r_ID__t0[1998_5_VN,Intercept] r_ID__t0[1998_6_VN,Intercept]
#> 1.0000695 0.9995852
#> r_ID__t0[1998_7_VN,Intercept] r_ID__t0[1998_73_VN,Intercept]
#> 0.9997503 0.9999764
#> r_ID__t0[1998_74_VN,Intercept] r_ID__t0[1998_76_VN,Intercept]
#> 0.9996036 1.0002056
#> r_ID__t0[1998_79_VN,Intercept] r_ID__t0[1998_8_VN,Intercept]
#> 0.9999988 0.9997330
#> r_ID__t0[1998_80_VN,Intercept] r_ID__t0[1998_87_VN,Intercept]
#> 0.9999252 0.9997988
#> r_ID__t0[1998_88_VN,Intercept] r_ID__t0[1998_9_VN,Intercept]
#> 0.9999233 1.0005278
#> r_ID__t0[1998_91_VN,Intercept] r_ID__t0[1998_92_VN,Intercept]
#> 1.0001915 1.0002958
#> r_ID__t0[1998_93_VN,Intercept] r_ID__t0[1998_94_VN,Intercept]
#> 0.9998297 1.0003042
#> r_ID__t0[1998_97_VN,Intercept] r_ID__t0[1998_99_VN,Intercept]
#> 0.9996938 1.0002341
#> r_ID__t0[1999_1_VN,Intercept] r_ID__t0[1999_10_VN,Intercept]
#> 1.0001043 0.9999073
#> r_ID__t0[1999_100_VN,Intercept] r_ID__t0[1999_101_VN,Intercept]
#> 0.9999794 1.0000553
#> r_ID__t0[1999_111_VN,Intercept] r_ID__t0[1999_112_VN,Intercept]
#> 0.9996851 1.0006014
#> r_ID__t0[1999_113_VN,Intercept] r_ID__t0[1999_115_VN,Intercept]
#> 0.9998178 0.9999075
#> r_ID__t0[1999_119_VN,Intercept] r_ID__t0[1999_122_VN,Intercept]
#> 0.9997406 1.0000212
#> r_ID__t0[1999_123_VN,Intercept] r_ID__t0[1999_125_VN,Intercept]
#> 0.9997981 0.9995664
#> r_ID__t0[1999_13_VN,Intercept] r_ID__t0[1999_133_VN,Intercept]
#> 0.9998144 0.9998446
#> r_ID__t0[1999_136_VN,Intercept] r_ID__t0[1999_137_VN,Intercept]
#> 1.0000508 0.9996112
#> r_ID__t0[1999_139_VN,Intercept] r_ID__t0[1999_150_VN,Intercept]
#> 0.9999002 0.9995645
#> r_ID__t0[1999_156_VN,Intercept] r_ID__t0[1999_16_VN,Intercept]
#> 0.9999646 0.9997685
#> r_ID__t0[1999_162_VN,Intercept] r_ID__t0[1999_166_VN,Intercept]
#> 0.9999310 0.9996482
#> r_ID__t0[1999_168_VN,Intercept] r_ID__t0[1999_170_VN,Intercept]
#> 1.0000544 0.9999371
#> r_ID__t0[1999_171_VN,Intercept] r_ID__t0[1999_18_VN,Intercept]
#> 0.9997259 0.9999137
#> r_ID__t0[1999_196_VN,Intercept] r_ID__t0[1999_198_VN,Intercept]
#> 0.9997998 0.9996834
#> r_ID__t0[1999_199_VN,Intercept] r_ID__t0[1999_2_VN,Intercept]
#> 1.0000114 1.0000204
#> r_ID__t0[1999_201_VN,Intercept] r_ID__t0[1999_202_VN,Intercept]
#> 0.9999783 1.0006219
#> r_ID__t0[1999_205_VN,Intercept] r_ID__t0[1999_210_VN,Intercept]
#> 0.9998869 1.0001509
#> r_ID__t0[1999_217_VN,Intercept] r_ID__t0[1999_219_VN,Intercept]
#> 0.9997916 0.9996991
#> r_ID__t0[1999_223_VN,Intercept] r_ID__t0[1999_238_VN,Intercept]
#> 0.9996902 0.9995709
#> r_ID__t0[1999_239_VN,Intercept] r_ID__t0[1999_248_VN,Intercept]
#> 0.9999156 0.9997085
#> r_ID__t0[1999_249_VN,Intercept] r_ID__t0[1999_280_VN,Intercept]
#> 0.9995963 0.9998215
#> r_ID__t0[1999_285_VN,Intercept] r_ID__t0[1999_32_VN,Intercept]
#> 1.0000677 0.9997765
#> r_ID__t0[1999_35_VN,Intercept] r_ID__t0[1999_36_VN,Intercept]
#> 0.9999219 0.9998040
#> r_ID__t0[1999_39_VN,Intercept] r_ID__t0[1999_4_VN,Intercept]
#> 1.0003877 1.0002081
#> r_ID__t0[1999_40_VN,Intercept] r_ID__t0[1999_46_VN,Intercept]
#> 1.0001443 0.9997663
#> r_ID__t0[1999_53_VN,Intercept] r_ID__t0[1999_54_VN,Intercept]
#> 0.9999330 0.9999196
#> r_ID__t0[1999_6_VN,Intercept] r_ID__t0[1999_62_VN,Intercept]
#> 0.9997444 1.0003612
#> r_ID__t0[1999_68_VN,Intercept] r_ID__t0[1999_75_VN,Intercept]
#> 1.0000320 1.0005456
#> r_ID__t0[1999_78_VN,Intercept] r_ID__t0[1999_8_VN,Intercept]
#> 0.9998364 0.9998805
#> r_ID__t0[1999_83_VN,Intercept] r_ID__t0[2000_153_VN,Intercept]
#> 1.0001675 0.9999710
#> r_ID__t0[2000_194_VN,Intercept] r_ID__t0[2000_225_VN,Intercept]
#> 0.9998916 1.0005338
#> r_ID__t0[2000_236_VN,Intercept] r_ID__t0[2000_246_VN,Intercept]
#> 0.9996208 0.9997277
#> r_ID__t0[2000_248_VN,Intercept] r_ID__t0[2000_265_VN,Intercept]
#> 0.9996762 0.9999808
#> r_ID__t0[2000_266_VN,Intercept] r_ID__t0[2000_87_VN,Intercept]
#> 0.9997607 1.0003940
#> r_ID__t0[2001_188_VN,Intercept] r_ID__t0[2001_242_VN,Intercept]
#> 0.9997539 0.9995850
#> r_ID__t0[2001_304_VN,Intercept] r_ID__t0[2001_308_VN,Intercept]
#> 0.9998129 1.0008046
#> r_ID__K[1996_246_VN,Intercept] r_ID__K[1997_102_VN,Intercept]
#> 1.0019971 1.0001627
#> r_ID__K[1997_105_VN,Intercept] r_ID__K[1997_106_VN,Intercept]
#> 0.9998623 1.0001165
#> r_ID__K[1997_107_VN,Intercept] r_ID__K[1997_108_VN,Intercept]
#> 0.9996135 1.0000055
#> r_ID__K[1997_109_VN,Intercept] r_ID__K[1997_11_VN,Intercept]
#> 1.0001278 0.9999860
#> r_ID__K[1997_110_VN,Intercept] r_ID__K[1997_113_VN,Intercept]
#> 1.0002434 1.0024368
#> r_ID__K[1997_115_VN,Intercept] r_ID__K[1997_12_VN,Intercept]
#> 1.0022615 0.9996886
#> r_ID__K[1997_13_VN,Intercept] r_ID__K[1997_14_VN,Intercept]
#> 0.9999451 1.0005573
#> r_ID__K[1997_15_VN,Intercept] r_ID__K[1997_151_VN,Intercept]
#> 1.0003605 1.0012558
#> r_ID__K[1997_152_VN,Intercept] r_ID__K[1997_153_VN,Intercept]
#> 1.0041733 0.9997724
#> r_ID__K[1997_156_VN,Intercept] r_ID__K[1997_157_VN,Intercept]
#> 1.0013665 0.9997884
#> r_ID__K[1997_159_VN,Intercept] r_ID__K[1997_160_VN,Intercept]
#> 1.0032983 1.0007280
#> r_ID__K[1997_162_VN,Intercept] r_ID__K[1997_17_VN,Intercept]
#> 0.9998474 1.0002958
#> r_ID__K[1997_18_VN,Intercept] r_ID__K[1997_189_VN,Intercept]
#> 1.0000863 1.0003358
#> r_ID__K[1997_19_VN,Intercept] r_ID__K[1997_190_VN,Intercept]
#> 1.0011219 0.9999132
#> r_ID__K[1997_192_VN,Intercept] r_ID__K[1997_193_VN,Intercept]
#> 1.0001686 0.9997779
#> r_ID__K[1997_195_VN,Intercept] r_ID__K[1997_199_VN,Intercept]
#> 0.9996790 0.9996761
#> r_ID__K[1997_20_VN,Intercept] r_ID__K[1997_201_VN,Intercept]
#> 0.9998388 1.0003869
#> r_ID__K[1997_21_VN,Intercept] r_ID__K[1997_211_VN,Intercept]
#> 0.9995256 0.9997901
#> r_ID__K[1997_212_VN,Intercept] r_ID__K[1997_213_VN,Intercept]
#> 0.9998835 1.0005185
#> r_ID__K[1997_217_VN,Intercept] r_ID__K[1997_218_VN,Intercept]
#> 1.0001499 1.0000391
#> r_ID__K[1997_219_VN,Intercept] r_ID__K[1997_220_VN,Intercept]
#> 0.9998669 1.0012271
#> r_ID__K[1997_222_VN,Intercept] r_ID__K[1997_223_VN,Intercept]
#> 0.9996592 1.0016339
#> r_ID__K[1997_226_VN,Intercept] r_ID__K[1997_227_VN,Intercept]
#> 1.0003377 0.9999231
#> r_ID__K[1997_229_VN,Intercept] r_ID__K[1997_23_VN,Intercept]
#> 1.0000244 0.9998010
#> r_ID__K[1997_230_VN,Intercept] r_ID__K[1997_235_VN,Intercept]
#> 1.0021051 1.0001713
#> r_ID__K[1997_236_VN,Intercept] r_ID__K[1997_240_VN,Intercept]
#> 0.9996299 1.0010494
#> r_ID__K[1997_241_VN,Intercept] r_ID__K[1997_244_VN,Intercept]
#> 0.9998999 1.0000280
#> r_ID__K[1997_248_VN,Intercept] r_ID__K[1997_250_VN,Intercept]
#> 1.0004901 0.9997731
#> r_ID__K[1997_252_VN,Intercept] r_ID__K[1997_253_VN,Intercept]
#> 1.0023745 1.0010045
#> r_ID__K[1997_254_VN,Intercept] r_ID__K[1997_256_VN,Intercept]
#> 1.0018138 0.9999552
#> r_ID__K[1997_257_VN,Intercept] r_ID__K[1997_258_VN,Intercept]
#> 1.0012576 1.0000061
#> r_ID__K[1997_263_VN,Intercept] r_ID__K[1997_268_VN,Intercept]
#> 1.0026651 1.0012107
#> r_ID__K[1997_270_VN,Intercept] r_ID__K[1997_271_VN,Intercept]
#> 1.0002169 1.0006401
#> r_ID__K[1998_102_VN,Intercept] r_ID__K[1998_103_VN,Intercept]
#> 1.0012807 0.9999101
#> r_ID__K[1998_11_VN,Intercept] r_ID__K[1998_110_VN,Intercept]
#> 1.0016689 1.0005107
#> r_ID__K[1998_111_VN,Intercept] r_ID__K[1998_12_VN,Intercept]
#> 1.0001565 1.0013508
#> r_ID__K[1998_121_VN,Intercept] r_ID__K[1998_122_VN,Intercept]
#> 1.0007409 0.9997424
#> r_ID__K[1998_123_VN,Intercept] r_ID__K[1998_124_VN,Intercept]
#> 0.9998455 0.9996591
#> r_ID__K[1998_125_VN,Intercept] r_ID__K[1998_127_VN,Intercept]
#> 0.9997867 1.0011196
#> r_ID__K[1998_128_VN,Intercept] r_ID__K[1998_129_VN,Intercept]
#> 1.0000424 0.9999520
#> r_ID__K[1998_13_VN,Intercept] r_ID__K[1998_138_VN,Intercept]
#> 1.0002135 1.0015181
#> r_ID__K[1998_14_VN,Intercept] r_ID__K[1998_140_VN,Intercept]
#> 0.9999433 1.0012444
#> r_ID__K[1998_143_VN,Intercept] r_ID__K[1998_145_VN,Intercept]
#> 1.0000385 0.9998083
#> r_ID__K[1998_146_VN,Intercept] r_ID__K[1998_148_VN,Intercept]
#> 0.9998358 1.0014123
#> r_ID__K[1998_149_VN,Intercept] r_ID__K[1998_155_VN,Intercept]
#> 1.0039394 1.0016860
#> r_ID__K[1998_17_VN,Intercept] r_ID__K[1998_273_VN,Intercept]
#> 1.0018693 1.0005752
#> r_ID__K[1998_285_VN,Intercept] r_ID__K[1998_288_VN,Intercept]
#> 1.0021029 1.0024020
#> r_ID__K[1998_289_VN,Intercept] r_ID__K[1998_29_VN,Intercept]
#> 1.0006490 1.0007586
#> r_ID__K[1998_290_VN,Intercept] r_ID__K[1998_291_VN,Intercept]
#> 0.9997290 0.9996331
#> r_ID__K[1998_292_VN,Intercept] r_ID__K[1998_295_VN,Intercept]
#> 0.9999533 1.0000296
#> r_ID__K[1998_3_VN,Intercept] r_ID__K[1998_30_VN,Intercept]
#> 1.0020408 1.0005340
#> r_ID__K[1998_303_VN,Intercept] r_ID__K[1998_304_VN,Intercept]
#> 1.0005300 1.0005693
#> r_ID__K[1998_305_VN,Intercept] r_ID__K[1998_306_VN,Intercept]
#> 1.0001946 1.0006876
#> r_ID__K[1998_31_VN,Intercept] r_ID__K[1998_315_VN,Intercept]
#> 0.9998687 1.0035628
#> r_ID__K[1998_32_VN,Intercept] r_ID__K[1998_323_VN,Intercept]
#> 1.0003645 1.0006697
#> r_ID__K[1998_327_VN,Intercept] r_ID__K[1998_329_VN,Intercept]
#> 1.0020329 0.9997760
#> r_ID__K[1998_33_VN,Intercept] r_ID__K[1998_330_VN,Intercept]
#> 1.0000321 1.0004690
#> r_ID__K[1998_332_VN,Intercept] r_ID__K[1998_333_VN,Intercept]
#> 1.0003256 1.0001165
#> r_ID__K[1998_334_VN,Intercept] r_ID__K[1998_335_VN,Intercept]
#> 1.0002639 0.9996337
#> r_ID__K[1998_336_VN,Intercept] r_ID__K[1998_337_VN,Intercept]
#> 0.9996370 1.0001802
#> r_ID__K[1998_338_VN,Intercept] r_ID__K[1998_339_VN,Intercept]
#> 0.9997104 1.0003023
#> r_ID__K[1998_34_VN,Intercept] r_ID__K[1998_340_VN,Intercept]
#> 0.9996947 1.0001975
#> r_ID__K[1998_341_VN,Intercept] r_ID__K[1998_342_VN,Intercept]
#> 1.0005419 0.9997748
#> r_ID__K[1998_343_VN,Intercept] r_ID__K[1998_349_VN,Intercept]
#> 0.9996246 1.0011598
#> r_ID__K[1998_35_VN,Intercept] r_ID__K[1998_352_VN,Intercept]
#> 0.9996480 1.0002018
#> r_ID__K[1998_36_VN,Intercept] r_ID__K[1998_37_VN,Intercept]
#> 0.9996134 1.0007525
#> r_ID__K[1998_397_VN,Intercept] r_ID__K[1998_4_VN,Intercept]
#> 1.0006511 1.0003304
#> r_ID__K[1998_400_VN,Intercept] r_ID__K[1998_401_VN,Intercept]
#> 1.0019269 0.9995243
#> r_ID__K[1998_402_VN,Intercept] r_ID__K[1998_407_VN,Intercept]
#> 1.0024318 1.0011282
#> r_ID__K[1998_45_VN,Intercept] r_ID__K[1998_5_VN,Intercept]
#> 1.0040820 1.0010624
#> r_ID__K[1998_6_VN,Intercept] r_ID__K[1998_7_VN,Intercept]
#> 1.0011088 1.0011766
#> r_ID__K[1998_73_VN,Intercept] r_ID__K[1998_74_VN,Intercept]
#> 0.9996219 1.0000461
#> r_ID__K[1998_76_VN,Intercept] r_ID__K[1998_79_VN,Intercept]
#> 1.0018614 0.9996764
#> r_ID__K[1998_8_VN,Intercept] r_ID__K[1998_80_VN,Intercept]
#> 1.0004556 1.0009226
#> r_ID__K[1998_87_VN,Intercept] r_ID__K[1998_88_VN,Intercept]
#> 1.0006333 1.0004828
#> r_ID__K[1998_9_VN,Intercept] r_ID__K[1998_91_VN,Intercept]
#> 1.0002605 1.0008123
#> r_ID__K[1998_92_VN,Intercept] r_ID__K[1998_93_VN,Intercept]
#> 0.9998002 0.9996915
#> r_ID__K[1998_94_VN,Intercept] r_ID__K[1998_97_VN,Intercept]
#> 0.9999139 1.0022326
#> r_ID__K[1998_99_VN,Intercept] r_ID__K[1999_1_VN,Intercept]
#> 0.9998635 1.0001939
#> r_ID__K[1999_10_VN,Intercept] r_ID__K[1999_100_VN,Intercept]
#> 1.0026441 1.0049297
#> r_ID__K[1999_101_VN,Intercept] r_ID__K[1999_111_VN,Intercept]
#> 1.0032254 0.9996250
#> r_ID__K[1999_112_VN,Intercept] r_ID__K[1999_113_VN,Intercept]
#> 1.0010952 0.9996727
#> r_ID__K[1999_115_VN,Intercept] r_ID__K[1999_119_VN,Intercept]
#> 0.9999672 1.0016326
#> r_ID__K[1999_122_VN,Intercept] r_ID__K[1999_123_VN,Intercept]
#> 1.0015988 1.0002483
#> r_ID__K[1999_125_VN,Intercept] r_ID__K[1999_13_VN,Intercept]
#> 1.0002239 0.9998456
#> r_ID__K[1999_133_VN,Intercept] r_ID__K[1999_136_VN,Intercept]
#> 1.0029616 0.9999208
#> r_ID__K[1999_137_VN,Intercept] r_ID__K[1999_139_VN,Intercept]
#> 1.0022503 1.0000519
#> r_ID__K[1999_150_VN,Intercept] r_ID__K[1999_156_VN,Intercept]
#> 1.0015921 0.9996111
#> r_ID__K[1999_16_VN,Intercept] r_ID__K[1999_162_VN,Intercept]
#> 0.9999073 1.0009508
#> r_ID__K[1999_166_VN,Intercept] r_ID__K[1999_168_VN,Intercept]
#> 1.0007039 1.0004267
#> r_ID__K[1999_170_VN,Intercept] r_ID__K[1999_171_VN,Intercept]
#> 0.9997113 1.0010819
#> r_ID__K[1999_18_VN,Intercept] r_ID__K[1999_196_VN,Intercept]
#> 0.9998536 1.0025570
#> r_ID__K[1999_198_VN,Intercept] r_ID__K[1999_199_VN,Intercept]
#> 1.0014541 1.0001055
#> r_ID__K[1999_2_VN,Intercept] r_ID__K[1999_201_VN,Intercept]
#> 0.9996810 0.9999787
#> r_ID__K[1999_202_VN,Intercept] r_ID__K[1999_205_VN,Intercept]
#> 0.9998685 1.0008260
#> r_ID__K[1999_210_VN,Intercept] r_ID__K[1999_217_VN,Intercept]
#> 1.0002533 1.0008103
#> r_ID__K[1999_219_VN,Intercept] r_ID__K[1999_223_VN,Intercept]
#> 1.0002649 1.0010683
#> r_ID__K[1999_238_VN,Intercept] r_ID__K[1999_239_VN,Intercept]
#> 1.0029035 0.9995692
#> r_ID__K[1999_248_VN,Intercept] r_ID__K[1999_249_VN,Intercept]
#> 1.0021599 1.0027954
#> r_ID__K[1999_280_VN,Intercept] r_ID__K[1999_285_VN,Intercept]
#> 1.0028744 1.0066131
#> r_ID__K[1999_32_VN,Intercept] r_ID__K[1999_35_VN,Intercept]
#> 0.9997401 0.9998592
#> r_ID__K[1999_36_VN,Intercept] r_ID__K[1999_39_VN,Intercept]
#> 1.0005395 1.0010799
#> r_ID__K[1999_4_VN,Intercept] r_ID__K[1999_40_VN,Intercept]
#> 1.0010051 1.0000757
#> r_ID__K[1999_46_VN,Intercept] r_ID__K[1999_53_VN,Intercept]
#> 1.0014343 1.0004585
#> r_ID__K[1999_54_VN,Intercept] r_ID__K[1999_6_VN,Intercept]
#> 1.0029311 1.0030515
#> r_ID__K[1999_62_VN,Intercept] r_ID__K[1999_68_VN,Intercept]
#> 1.0017327 1.0022550
#> r_ID__K[1999_75_VN,Intercept] r_ID__K[1999_78_VN,Intercept]
#> 1.0009406 1.0001708
#> r_ID__K[1999_8_VN,Intercept] r_ID__K[1999_83_VN,Intercept]
#> 0.9996732 1.0008066
#> r_ID__K[2000_153_VN,Intercept] r_ID__K[2000_194_VN,Intercept]
#> 1.0009409 0.9995946
#> r_ID__K[2000_225_VN,Intercept] r_ID__K[2000_236_VN,Intercept]
#> 1.0027129 0.9997864
#> r_ID__K[2000_246_VN,Intercept] r_ID__K[2000_248_VN,Intercept]
#> 0.9998575 0.9999193
#> r_ID__K[2000_265_VN,Intercept] r_ID__K[2000_266_VN,Intercept]
#> 1.0006764 0.9998525
#> r_ID__K[2000_87_VN,Intercept] r_ID__K[2001_188_VN,Intercept]
#> 1.0013540 1.0016925
#> r_ID__K[2001_242_VN,Intercept] r_ID__K[2001_304_VN,Intercept]
#> 1.0007992 1.0006237
#> r_ID__K[2001_308_VN,Intercept] r_ID__Linf[1996_246_VN,Intercept]
#> 1.0033302 0.9996058
#> r_ID__Linf[1997_102_VN,Intercept] r_ID__Linf[1997_105_VN,Intercept]
#> 0.9996311 0.9999965
#> r_ID__Linf[1997_106_VN,Intercept] r_ID__Linf[1997_107_VN,Intercept]
#> 0.9996311 0.9998474
#> r_ID__Linf[1997_108_VN,Intercept] r_ID__Linf[1997_109_VN,Intercept]
#> 0.9997632 0.9995606
#> r_ID__Linf[1997_11_VN,Intercept] r_ID__Linf[1997_110_VN,Intercept]
#> 0.9996808 0.9999675
#> r_ID__Linf[1997_113_VN,Intercept] r_ID__Linf[1997_115_VN,Intercept]
#> 0.9997644 1.0008508
#> r_ID__Linf[1997_12_VN,Intercept] r_ID__Linf[1997_13_VN,Intercept]
#> 0.9997662 0.9996919
#> r_ID__Linf[1997_14_VN,Intercept] r_ID__Linf[1997_15_VN,Intercept]
#> 1.0001366 1.0001124
#> r_ID__Linf[1997_151_VN,Intercept] r_ID__Linf[1997_152_VN,Intercept]
#> 1.0001516 1.0002094
#> r_ID__Linf[1997_153_VN,Intercept] r_ID__Linf[1997_156_VN,Intercept]
#> 0.9996471 1.0005465
#> r_ID__Linf[1997_157_VN,Intercept] r_ID__Linf[1997_159_VN,Intercept]
#> 0.9998547 1.0002812
#> r_ID__Linf[1997_160_VN,Intercept] r_ID__Linf[1997_162_VN,Intercept]
#> 1.0002928 0.9996275
#> r_ID__Linf[1997_17_VN,Intercept] r_ID__Linf[1997_18_VN,Intercept]
#> 0.9998350 1.0003166
#> r_ID__Linf[1997_189_VN,Intercept] r_ID__Linf[1997_19_VN,Intercept]
#> 0.9997421 0.9999849
#> r_ID__Linf[1997_190_VN,Intercept] r_ID__Linf[1997_192_VN,Intercept]
#> 0.9999647 1.0006271
#> r_ID__Linf[1997_193_VN,Intercept] r_ID__Linf[1997_195_VN,Intercept]
#> 0.9996039 0.9995818
#> r_ID__Linf[1997_199_VN,Intercept] r_ID__Linf[1997_20_VN,Intercept]
#> 0.9999738 0.9999406
#> r_ID__Linf[1997_201_VN,Intercept] r_ID__Linf[1997_21_VN,Intercept]
#> 0.9997996 0.9998314
#> r_ID__Linf[1997_211_VN,Intercept] r_ID__Linf[1997_212_VN,Intercept]
#> 0.9998472 0.9996576
#> r_ID__Linf[1997_213_VN,Intercept] r_ID__Linf[1997_217_VN,Intercept]
#> 1.0001243 0.9996521
#> r_ID__Linf[1997_218_VN,Intercept] r_ID__Linf[1997_219_VN,Intercept]
#> 0.9997518 0.9998740
#> r_ID__Linf[1997_220_VN,Intercept] r_ID__Linf[1997_222_VN,Intercept]
#> 0.9995885 1.0005453
#> r_ID__Linf[1997_223_VN,Intercept] r_ID__Linf[1997_226_VN,Intercept]
#> 1.0004322 0.9996333
#> r_ID__Linf[1997_227_VN,Intercept] r_ID__Linf[1997_229_VN,Intercept]
#> 0.9998751 1.0002331
#> r_ID__Linf[1997_23_VN,Intercept] r_ID__Linf[1997_230_VN,Intercept]
#> 0.9999095 1.0001175
#> r_ID__Linf[1997_235_VN,Intercept] r_ID__Linf[1997_236_VN,Intercept]
#> 0.9998026 0.9997271
#> r_ID__Linf[1997_240_VN,Intercept] r_ID__Linf[1997_241_VN,Intercept]
#> 0.9998616 1.0003856
#> r_ID__Linf[1997_244_VN,Intercept] r_ID__Linf[1997_248_VN,Intercept]
#> 1.0000888 0.9995493
#> r_ID__Linf[1997_250_VN,Intercept] r_ID__Linf[1997_252_VN,Intercept]
#> 0.9998654 0.9999841
#> r_ID__Linf[1997_253_VN,Intercept] r_ID__Linf[1997_254_VN,Intercept]
#> 1.0000787 0.9996955
#> r_ID__Linf[1997_256_VN,Intercept] r_ID__Linf[1997_257_VN,Intercept]
#> 0.9996122 1.0003143
#> r_ID__Linf[1997_258_VN,Intercept] r_ID__Linf[1997_263_VN,Intercept]
#> 0.9999533 0.9998847
#> r_ID__Linf[1997_268_VN,Intercept] r_ID__Linf[1997_270_VN,Intercept]
#> 0.9998679 0.9999480
#> r_ID__Linf[1997_271_VN,Intercept] r_ID__Linf[1998_102_VN,Intercept]
#> 0.9995286 1.0000444
#> r_ID__Linf[1998_103_VN,Intercept] r_ID__Linf[1998_11_VN,Intercept]
#> 0.9998182 0.9999812
#> r_ID__Linf[1998_110_VN,Intercept] r_ID__Linf[1998_111_VN,Intercept]
#> 1.0000615 0.9996101
#> r_ID__Linf[1998_12_VN,Intercept] r_ID__Linf[1998_121_VN,Intercept]
#> 1.0008435 1.0002775
#> r_ID__Linf[1998_122_VN,Intercept] r_ID__Linf[1998_123_VN,Intercept]
#> 1.0000101 0.9997121
#> r_ID__Linf[1998_124_VN,Intercept] r_ID__Linf[1998_125_VN,Intercept]
#> 0.9996054 1.0002174
#> r_ID__Linf[1998_127_VN,Intercept] r_ID__Linf[1998_128_VN,Intercept]
#> 1.0005400 0.9996591
#> r_ID__Linf[1998_129_VN,Intercept] r_ID__Linf[1998_13_VN,Intercept]
#> 0.9996065 0.9999954
#> r_ID__Linf[1998_138_VN,Intercept] r_ID__Linf[1998_14_VN,Intercept]
#> 0.9997264 0.9999701
#> r_ID__Linf[1998_140_VN,Intercept] r_ID__Linf[1998_143_VN,Intercept]
#> 1.0004280 1.0004264
#> r_ID__Linf[1998_145_VN,Intercept] r_ID__Linf[1998_146_VN,Intercept]
#> 0.9996381 0.9995782
#> r_ID__Linf[1998_148_VN,Intercept] r_ID__Linf[1998_149_VN,Intercept]
#> 1.0001802 1.0016041
#> r_ID__Linf[1998_155_VN,Intercept] r_ID__Linf[1998_17_VN,Intercept]
#> 0.9999860 1.0006521
#> r_ID__Linf[1998_273_VN,Intercept] r_ID__Linf[1998_285_VN,Intercept]
#> 1.0002502 1.0002199
#> r_ID__Linf[1998_288_VN,Intercept] r_ID__Linf[1998_289_VN,Intercept]
#> 1.0003320 1.0004620
#> r_ID__Linf[1998_29_VN,Intercept] r_ID__Linf[1998_290_VN,Intercept]
#> 1.0001888 1.0000477
#> r_ID__Linf[1998_291_VN,Intercept] r_ID__Linf[1998_292_VN,Intercept]
#> 0.9996377 0.9997033
#> r_ID__Linf[1998_295_VN,Intercept] r_ID__Linf[1998_3_VN,Intercept]
#> 0.9995406 0.9997839
#> r_ID__Linf[1998_30_VN,Intercept] r_ID__Linf[1998_303_VN,Intercept]
#> 1.0004183 0.9998191
#> r_ID__Linf[1998_304_VN,Intercept] r_ID__Linf[1998_305_VN,Intercept]
#> 1.0000995 0.9995833
#> r_ID__Linf[1998_306_VN,Intercept] r_ID__Linf[1998_31_VN,Intercept]
#> 1.0002265 0.9997450
#> r_ID__Linf[1998_315_VN,Intercept] r_ID__Linf[1998_32_VN,Intercept]
#> 1.0005323 0.9999083
#> r_ID__Linf[1998_323_VN,Intercept] r_ID__Linf[1998_327_VN,Intercept]
#> 0.9998473 1.0007298
#> r_ID__Linf[1998_329_VN,Intercept] r_ID__Linf[1998_33_VN,Intercept]
#> 1.0001752 0.9997841
#> r_ID__Linf[1998_330_VN,Intercept] r_ID__Linf[1998_332_VN,Intercept]
#> 0.9997092 1.0002116
#> r_ID__Linf[1998_333_VN,Intercept] r_ID__Linf[1998_334_VN,Intercept]
#> 0.9998620 0.9999319
#> r_ID__Linf[1998_335_VN,Intercept] r_ID__Linf[1998_336_VN,Intercept]
#> 0.9998973 0.9997740
#> r_ID__Linf[1998_337_VN,Intercept] r_ID__Linf[1998_338_VN,Intercept]
#> 0.9998496 0.9998509
#> r_ID__Linf[1998_339_VN,Intercept] r_ID__Linf[1998_34_VN,Intercept]
#> 0.9998043 0.9996842
#> r_ID__Linf[1998_340_VN,Intercept] r_ID__Linf[1998_341_VN,Intercept]
#> 0.9999755 1.0004148
#> r_ID__Linf[1998_342_VN,Intercept] r_ID__Linf[1998_343_VN,Intercept]
#> 0.9997059 0.9999476
#> r_ID__Linf[1998_349_VN,Intercept] r_ID__Linf[1998_35_VN,Intercept]
#> 1.0000158 0.9998195
#> r_ID__Linf[1998_352_VN,Intercept] r_ID__Linf[1998_36_VN,Intercept]
#> 0.9998970 0.9995988
#> r_ID__Linf[1998_37_VN,Intercept] r_ID__Linf[1998_397_VN,Intercept]
#> 0.9996501 0.9999873
#> r_ID__Linf[1998_4_VN,Intercept] r_ID__Linf[1998_400_VN,Intercept]
#> 1.0000510 1.0011179
#> r_ID__Linf[1998_401_VN,Intercept] r_ID__Linf[1998_402_VN,Intercept]
#> 0.9998632 0.9998530
#> r_ID__Linf[1998_407_VN,Intercept] r_ID__Linf[1998_45_VN,Intercept]
#> 1.0004664 1.0003802
#> r_ID__Linf[1998_5_VN,Intercept] r_ID__Linf[1998_6_VN,Intercept]
#> 1.0003279 1.0002825
#> r_ID__Linf[1998_7_VN,Intercept] r_ID__Linf[1998_73_VN,Intercept]
#> 1.0008239 0.9999234
#> r_ID__Linf[1998_74_VN,Intercept] r_ID__Linf[1998_76_VN,Intercept]
#> 0.9998695 0.9998534
#> r_ID__Linf[1998_79_VN,Intercept] r_ID__Linf[1998_8_VN,Intercept]
#> 0.9996882 0.9999222
#> r_ID__Linf[1998_80_VN,Intercept] r_ID__Linf[1998_87_VN,Intercept]
#> 0.9997401 1.0000858
#> r_ID__Linf[1998_88_VN,Intercept] r_ID__Linf[1998_9_VN,Intercept]
#> 0.9997311 0.9998601
#> r_ID__Linf[1998_91_VN,Intercept] r_ID__Linf[1998_92_VN,Intercept]
#> 1.0000530 1.0001972
#> r_ID__Linf[1998_93_VN,Intercept] r_ID__Linf[1998_94_VN,Intercept]
#> 0.9998906 0.9999337
#> r_ID__Linf[1998_97_VN,Intercept] r_ID__Linf[1998_99_VN,Intercept]
#> 1.0012621 0.9997914
#> r_ID__Linf[1999_1_VN,Intercept] r_ID__Linf[1999_10_VN,Intercept]
#> 0.9997421 1.0010366
#> r_ID__Linf[1999_100_VN,Intercept] r_ID__Linf[1999_101_VN,Intercept]
#> 1.0016346 1.0014334
#> r_ID__Linf[1999_111_VN,Intercept] r_ID__Linf[1999_112_VN,Intercept]
#> 0.9997910 1.0003894
#> r_ID__Linf[1999_113_VN,Intercept] r_ID__Linf[1999_115_VN,Intercept]
#> 0.9999640 0.9997126
#> r_ID__Linf[1999_119_VN,Intercept] r_ID__Linf[1999_122_VN,Intercept]
#> 1.0001734 1.0001870
#> r_ID__Linf[1999_123_VN,Intercept] r_ID__Linf[1999_125_VN,Intercept]
#> 0.9999472 1.0005829
#> r_ID__Linf[1999_13_VN,Intercept] r_ID__Linf[1999_133_VN,Intercept]
#> 0.9996095 1.0000563
#> r_ID__Linf[1999_136_VN,Intercept] r_ID__Linf[1999_137_VN,Intercept]
#> 0.9997365 1.0002269
#> r_ID__Linf[1999_139_VN,Intercept] r_ID__Linf[1999_150_VN,Intercept]
#> 1.0001023 1.0003604
#> r_ID__Linf[1999_156_VN,Intercept] r_ID__Linf[1999_16_VN,Intercept]
#> 0.9998426 0.9996224
#> r_ID__Linf[1999_162_VN,Intercept] r_ID__Linf[1999_166_VN,Intercept]
#> 1.0000985 0.9996246
#> r_ID__Linf[1999_168_VN,Intercept] r_ID__Linf[1999_170_VN,Intercept]
#> 1.0000318 1.0002087
#> r_ID__Linf[1999_171_VN,Intercept] r_ID__Linf[1999_18_VN,Intercept]
#> 0.9999132 0.9996419
#> r_ID__Linf[1999_196_VN,Intercept] r_ID__Linf[1999_198_VN,Intercept]
#> 1.0009676 1.0001625
#> r_ID__Linf[1999_199_VN,Intercept] r_ID__Linf[1999_2_VN,Intercept]
#> 0.9996115 0.9998168
#> r_ID__Linf[1999_201_VN,Intercept] r_ID__Linf[1999_202_VN,Intercept]
#> 0.9998040 0.9996328
#> r_ID__Linf[1999_205_VN,Intercept] r_ID__Linf[1999_210_VN,Intercept]
#> 1.0006817 1.0000067
#> r_ID__Linf[1999_217_VN,Intercept] r_ID__Linf[1999_219_VN,Intercept]
#> 1.0007132 1.0003194
#> r_ID__Linf[1999_223_VN,Intercept] r_ID__Linf[1999_238_VN,Intercept]
#> 1.0001104 1.0002551
#> r_ID__Linf[1999_239_VN,Intercept] r_ID__Linf[1999_248_VN,Intercept]
#> 0.9996675 1.0003586
#> r_ID__Linf[1999_249_VN,Intercept] r_ID__Linf[1999_280_VN,Intercept]
#> 1.0013251 0.9997276
#> r_ID__Linf[1999_285_VN,Intercept] r_ID__Linf[1999_32_VN,Intercept]
#> 1.0024552 0.9998228
#> r_ID__Linf[1999_35_VN,Intercept] r_ID__Linf[1999_36_VN,Intercept]
#> 1.0001085 1.0000934
#> r_ID__Linf[1999_39_VN,Intercept] r_ID__Linf[1999_4_VN,Intercept]
#> 1.0004627 1.0004367
#> r_ID__Linf[1999_40_VN,Intercept] r_ID__Linf[1999_46_VN,Intercept]
#> 1.0003242 1.0001227
#> r_ID__Linf[1999_53_VN,Intercept] r_ID__Linf[1999_54_VN,Intercept]
#> 1.0005257 1.0017512
#> r_ID__Linf[1999_6_VN,Intercept] r_ID__Linf[1999_62_VN,Intercept]
#> 1.0007951 1.0009803
#> r_ID__Linf[1999_68_VN,Intercept] r_ID__Linf[1999_75_VN,Intercept]
#> 1.0011974 1.0001762
#> r_ID__Linf[1999_78_VN,Intercept] r_ID__Linf[1999_8_VN,Intercept]
#> 1.0004856 1.0002548
#> r_ID__Linf[1999_83_VN,Intercept] r_ID__Linf[2000_153_VN,Intercept]
#> 1.0001460 1.0015146
#> r_ID__Linf[2000_194_VN,Intercept] r_ID__Linf[2000_225_VN,Intercept]
#> 0.9998187 1.0013636
#> r_ID__Linf[2000_236_VN,Intercept] r_ID__Linf[2000_246_VN,Intercept]
#> 0.9995822 1.0000530
#> r_ID__Linf[2000_248_VN,Intercept] r_ID__Linf[2000_265_VN,Intercept]
#> 1.0000436 1.0007115
#> r_ID__Linf[2000_266_VN,Intercept] r_ID__Linf[2000_87_VN,Intercept]
#> 0.9997598 0.9997350
#> r_ID__Linf[2001_188_VN,Intercept] r_ID__Linf[2001_242_VN,Intercept]
#> 1.0004706 1.0003130
#> r_ID__Linf[2001_304_VN,Intercept] r_ID__Linf[2001_308_VN,Intercept]
#> 1.0002635 1.0026799
#> lprior lp__
#> 0.9999686 1.0034517
plot(mtest)
summary(mtest)
#> Family: gaussian
#> Links: mu = identity; sigma = identity
#> Formula: length_cm ~ Linf * (1 - exp(-K * (age_bc - t0)))
#> t0 ~ 1 + (1 | ID)
#> K ~ 1 + (1 | ID)
#> Linf ~ 1 + (1 | ID)
#> Data: filter(d_vin, cohort == 1995) (Number of observations: 938)
#> Draws: 3 chains, each with iter = 4000; warmup = 2000; thin = 1;
#> total post-warmup draws = 6000
#>
#> Group-Level Effects:
#> ~ID (Number of levels: 229)
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> sd(t0_Intercept) 0.02 0.01 0.00 0.05 1.00 1544 2370
#> sd(K_Intercept) 0.00 0.00 0.00 0.01 1.01 167 545
#> sd(Linf_Intercept) 4.32 0.40 3.61 5.19 1.00 1476 2727
#>
#> Population-Level Effects:
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> t0_Intercept -0.22 0.04 -0.29 -0.14 1.00 3096 3214
#> K_Intercept 0.12 0.01 0.10 0.14 1.00 2633 3161
#> Linf_Intercept 48.67 3.14 43.18 55.40 1.00 2603 3334
#>
#> Family Specific Parameters:
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> sigma 1.09 0.03 1.03 1.15 1.00 5267 4140
#>
#> Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
#> and Tail_ESS are effective sample size measures, and Rhat is the potential
#> scale reduction factor on split chains (at convergence, Rhat = 1).
# Plot predictions by ID
d_vin %>%
filter(cohort == 1995) %>%
add_predicted_draws(mtest) %>%
ggplot(aes(x = age_bc, y = length_cm, color = ID, fill = ID)) +
stat_lineribbon(aes(y = .prediction, group = ID), .width = .95, alpha = 0.1, size = 0.5) +
stat_lineribbon(aes(y = .prediction, group = ID), .width = 0, alpha = 0.5, size = 0.5) +
geom_jitter(data = filter(d_vin, cohort == 1995),
width = 0.3, height = 0, size = 2) +
scale_fill_viridis(discrete = TRUE) +
scale_color_viridis(discrete = TRUE) +
labs(y = "Length [cm]", x = "Age [yrs]", fill = "ID", colour = "ID") +
guides(color = "none", fill = "none") +
NULL
# Plot global predictions
d_vin %>%
filter(cohort == 1995) %>%
data_grid(age_bc = seq_range(age_bc, by = 1)) %>%
add_predicted_draws(mtest, re_formula = NA) %>%
ggplot(aes(x = age_bc, y = length_cm)) +
stat_lineribbon(aes(y = .prediction), .width = .95, alpha = 0.4) +
geom_jitter(data = filter(d_vin, cohort == 1995),
alpha = 0.1, width = 0.3,
height = 0, size = 2) +
labs(y = "Length [cm]", x = "Age [yrs]") +
NULL
# Plot individual-level parameters
get_variables(mtest)
# t0
mtest %>%
spread_draws(b_t0_Intercept,
r_ID__t0[ID, Intercept]) %>%
mutate(mean_t0 = b_t0_Intercept + r_ID__t0) %>% # The random effects are offsets
ggplot(aes(y = factor(ID), x = mean_t0)) +
stat_pointinterval(.width = 0.95, alpha = 0.2) +
theme(axis.text.y = element_text(size = 3)) +
ggtitle("ID-level t0 with 50% credible interval (global in red)") +
geom_vline(xintercept = mean(spread_draws(mtest, b_t0_Intercept)$b_t0_Intercept),
color = "tomato", linetype = 2) +
NULL
# K
mtest %>%
spread_draws(b_K_Intercept,
r_ID__K[ID, Intercept]) %>%
mutate(mean_K = b_K_Intercept + r_ID__K) %>% # The random effects are offsets
ggplot(aes(y = factor(ID), x = mean_K)) +
stat_pointinterval(.width = 0.95, alpha = 0.2) +
theme(axis.text.y = element_text(size = 3)) +
ggtitle("ID-level K with 50% credible interval (global in red)") +
geom_vline(xintercept = mean(spread_draws(mtest, b_K_Intercept)$b_K_Intercept),
color = "tomato", linetype = 2) +
NULL
# L_inf
mtest %>%
spread_draws(b_Linf_Intercept,
r_ID__Linf[ID, Intercept]) %>%
mutate(mean_Linf = b_Linf_Intercept + r_ID__Linf) %>% # The random effects are offsets
ggplot(aes(y = factor(ID), x = mean_Linf)) +
stat_pointinterval(.width = 0.95, alpha = 0.2) +
theme(axis.text.y = element_text(size = 3)) +
ggtitle("ID-level Linf with 50% credible interval (global in red)") +
geom_vline(xintercept = mean(spread_draws(mtest, b_Linf_Intercept)$b_Linf_Intercept),
color = "tomato", linetype = 2) +
NULL
Ok, good enough. Now loop through all cohorts and fit the same model, summarize quantiles of each cohorts parameter estimates and save in a dataframe
ggplot(filter(d, age_catch < 5), aes(age_bc, length_cm)) +
geom_point()
#> filter: removed 166,986 rows (46%), 196,156 rows remaining
# Fit model with parameters varying by ID. First filter a single year to test speed
quant_list <- list()
d$area_cohort_id <- paste(d$area, d$cohort, sep = "_")
for(i in unique(d$area_cohort_id)) {
dd <- filter(d, area_cohort_id == i)
m <-
brm(
bf(length_cm ~ Linf*(1-exp(-K*(age_bc-t0))),
t0 ~ 1 + (1|ID),
K ~ 1 + (1|ID),
Linf ~ 1 + (1|ID),
nl = TRUE),
data = dd,
family = gaussian(),
prior = c(prior(normal(45, 20), nlpar = "Linf"),
prior(normal(-0.5, 1), nlpar = "t0"),
prior(normal(0.2, 0.1), nlpar = "K")),
iter = 3000,
thin = 1,
cores = 3,
chains = 3,
seed = 9)
quants <- m %>%
spread_draws(b_Linf_Intercept, b_K_Intercept) %>%
summarise(K_01 = quantile(b_K_Intercept, probs = 0.1),
K_025 = quantile(b_K_Intercept, probs = 0.25),
K_05 = quantile(b_K_Intercept, probs = 0.5),
K_075 = quantile(b_K_Intercept, probs = 0.75),
K_09 = quantile(b_K_Intercept, probs = 0.9),
Linf_01 = quantile(b_Linf_Intercept, probs = 0.1),
Linf_025 = quantile(b_Linf_Intercept, probs = 0.25),
Linf_05 = quantile(b_Linf_Intercept, probs = 0.5),
Linf_075 = quantile(b_Linf_Intercept, probs = 0.75),
Linf_09 = quantile(b_Linf_Intercept, probs = 0.9)) %>%
mutate(max_rhat = round(max(rhat(m)), digits = 3)) %>%
as.data.frame()
list_pos_q1 <- as.numeric(as.factor(i))
quant_list[[i]] <- quants
}
#> filter: removed 362,707 rows (>99%), 435 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,258 rows (>99%), 884 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,332 rows (>99%), 810 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.07, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,168 rows (>99%), 974 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,047 rows (>99%), 95 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 44 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1364 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,894 rows (>99%), 248 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 53 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1447 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,891 rows (>99%), 251 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,657 rows (>99%), 485 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,086 rows (>99%), 1,056 rows remaining
#> Compiling Stan program...
#> recompiling to avoid crashing R session
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,837 rows (>99%), 305 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 398 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.75, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,339 rows (>99%), 803 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,736 rows (>99%), 406 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,165 rows (>99%), 977 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1495 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.78, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,302 rows (>99%), 840 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,429 rows (>99%), 713 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,318 rows (>99%), 824 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,190 rows (>99%), 952 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,063 rows (>99%), 1,079 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,530 rows (>99%), 612 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.77, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,227 rows (>99%), 915 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 17 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,901 rows (>99%), 1,241 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 16 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,299 rows (>99%), 843 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 102 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,232 rows (>99%), 910 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,415 rows (>99%), 727 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,448 rows (>99%), 694 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 24 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,762 rows (>99%), 380 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,558 rows (>99%), 584 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 66 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,634 rows (>99%), 508 rows remaining
#> Compiling Stan program...
#> recompiling to avoid crashing R session
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,699 rows (>99%), 443 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 14 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,319 rows (>99%), 823 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,812 rows (>99%), 330 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 35 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 2 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,863 rows (>99%), 279 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,935 rows (>99%), 207 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,613 rows (>99%), 529 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,548 rows (>99%), 594 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.38, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,467 rows (>99%), 675 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.39, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,806 rows (>99%), 336 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,873 rows (>99%), 269 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,866 rows (>99%), 276 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,970 rows (>99%), 172 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,975 rows (>99%), 167 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,840 rows (>99%), 302 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,752 rows (>99%), 390 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,038 rows (>99%), 104 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,968 rows (>99%), 174 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,123 rows (>99%), 19 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 129 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,036 rows (>99%), 106 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,038 rows (>99%), 104 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 408 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.94, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,088 rows (>99%), 54 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 199 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 881 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 2 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,939 rows (>99%), 1,203 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 11 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,594 rows (>99%), 1,548 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,513 rows (>99%), 629 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,382 rows (>99%), 1,760 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,836 rows (>99%), 1,306 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.76, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,696 rows (>99%), 1,446 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,915 rows (>99%), 227 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 26 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.38, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,013 rows (>99%), 1,129 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,258 rows (99%), 1,884 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,651 rows (>99%), 491 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,964 rows (>99%), 178 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,042 rows (>99%), 100 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 133 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 18 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.36, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 359,297 rows (99%), 3,845 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 35 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,328 rows (>99%), 814 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 14 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.7, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,771 rows (>99%), 371 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,025 rows (>99%), 117 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,349 rows (>99%), 793 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,069 rows (>99%), 1,073 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.87, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,525 rows (>99%), 1,617 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,777 rows (>99%), 1,365 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,655 rows (>99%), 487 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,390 rows (>99%), 752 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,048 rows (>99%), 1,094 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,868 rows (>99%), 274 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,331 rows (>99%), 811 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 2 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,830 rows (>99%), 312 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 10 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,038 rows (>99%), 104 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 144 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 167 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,392 rows (>99%), 750 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,595 rows (>99%), 547 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,920 rows (>99%), 222 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 395 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.92, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,715 rows (>99%), 427 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.38, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,531 rows (>99%), 611 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,611 rows (>99%), 1,531 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,234 rows (>99%), 908 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 8 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,698 rows (>99%), 1,444 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,394 rows (>99%), 1,748 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.77, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,806 rows (99%), 2,336 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 397 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.03, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,702 rows (>99%), 1,440 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1332 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 168 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,243 rows (>99%), 899 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,437 rows (>99%), 1,705 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 359,545 rows (99%), 3,597 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.73, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,256 rows (99%), 1,886 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,680 rows (>99%), 1,462 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.09, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,662 rows (>99%), 1,480 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 9 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,372 rows (>99%), 1,770 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,202 rows (>99%), 940 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,267 rows (99%), 2,875 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,622 rows (>99%), 1,520 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 5 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,723 rows (>99%), 1,419 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 359,881 rows (99%), 3,261 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 539 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 961 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,550 rows (>99%), 592 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,660 rows (99%), 2,482 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,075 rows (99%), 2,067 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 93 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1407 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,512 rows (>99%), 1,630 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,431 rows (99%), 2,711 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 414 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1104 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.76, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,003 rows (>99%), 1,139 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,783 rows (99%), 2,359 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,472 rows (>99%), 670 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,363 rows (>99%), 779 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,671 rows (>99%), 1,471 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,089 rows (99%), 2,053 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 901 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 629 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.79, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,012 rows (>99%), 1,130 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 4 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,795 rows (99%), 2,347 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,448 rows (>99%), 1,694 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,262 rows (>99%), 880 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,832 rows (>99%), 1,310 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,968 rows (>99%), 1,174 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,542 rows (>99%), 600 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,516 rows (>99%), 626 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,879 rows (>99%), 263 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,994 rows (>99%), 148 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 6 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,104 rows (>99%), 38 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 845 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.05, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,895 rows (>99%), 247 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,959 rows (>99%), 183 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 4410 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.47, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,688 rows (>99%), 454 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,868 rows (>99%), 274 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,216 rows (>99%), 926 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,230 rows (99%), 1,912 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,970 rows (>99%), 1,172 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 612 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,420 rows (>99%), 722 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,576 rows (>99%), 1,566 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 19 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 358,545 rows (99%), 4,597 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,827 rows (>99%), 1,315 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.75, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,648 rows (99%), 2,494 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,180 rows (>99%), 962 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,779 rows (>99%), 363 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1363 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,602 rows (>99%), 540 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,812 rows (>99%), 330 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 82 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,277 rows (>99%), 865 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 8 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,653 rows (>99%), 1,489 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,547 rows (99%), 2,595 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 446 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1054 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,795 rows (>99%), 1,347 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1499 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,228 rows (99%), 1,914 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,581 rows (>99%), 1,561 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,105 rows (>99%), 1,037 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.07, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,094 rows (>99%), 1,048 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,915 rows (>99%), 1,227 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,160 rows (99%), 1,982 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,656 rows (>99%), 1,486 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 17 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,889 rows (99%), 2,253 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1499 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.91, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,932 rows (99%), 2,210 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 4 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,099 rows (99%), 2,043 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 24 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,722 rows (>99%), 1,420 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.21, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,040 rows (99%), 2,102 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 427 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 2573 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,485 rows (>99%), 1,657 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 9 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1499 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,906 rows (>99%), 1,236 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 4 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,578 rows (>99%), 1,564 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,376 rows (>99%), 766 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,327 rows (>99%), 815 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,303 rows (>99%), 839 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,478 rows (>99%), 1,664 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 15 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,754 rows (>99%), 1,388 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,123 rows (>99%), 1,019 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,871 rows (>99%), 1,271 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,082 rows (>99%), 1,060 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 62 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,049 rows (>99%), 1,093 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,106 rows (99%), 2,036 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,750 rows (>99%), 1,392 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,836 rows (>99%), 306 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,471 rows (>99%), 1,671 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,437 rows (>99%), 705 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,534 rows (>99%), 608 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,199 rows (99%), 1,943 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,104 rows (>99%), 1,038 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 48 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 31 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.74, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,920 rows (>99%), 222 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 30 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.2, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,446 rows (>99%), 696 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,280 rows (>99%), 862 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,868 rows (>99%), 1,274 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,769 rows (>99%), 1,373 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,517 rows (>99%), 625 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,257 rows (>99%), 885 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,792 rows (>99%), 350 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,761 rows (>99%), 381 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,709 rows (>99%), 433 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,945 rows (>99%), 197 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1802 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.36, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,576 rows (99%), 2,566 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.78, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,597 rows (>99%), 545 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,912 rows (>99%), 1,230 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,965 rows (>99%), 1,177 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,779 rows (>99%), 363 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,328 rows (>99%), 814 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,470 rows (>99%), 672 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.1, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,817 rows (>99%), 325 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1524 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,735 rows (>99%), 1,407 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,605 rows (>99%), 537 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.7, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,097 rows (>99%), 1,045 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,661 rows (>99%), 481 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,760 rows (>99%), 1,382 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,265 rows (>99%), 877 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 11 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,476 rows (>99%), 666 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,485 rows (>99%), 1,657 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.51, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,670 rows (>99%), 472 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.76, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,881 rows (>99%), 261 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,351 rows (>99%), 791 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,042 rows (>99%), 1,100 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,505 rows (>99%), 637 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,473 rows (>99%), 669 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.15, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,468 rows (>99%), 674 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,403 rows (>99%), 739 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,814 rows (>99%), 328 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,538 rows (>99%), 604 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,516 rows (>99%), 626 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,691 rows (>99%), 451 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,685 rows (>99%), 457 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.09, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,913 rows (>99%), 229 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,868 rows (>99%), 274 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 11 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 113 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,091 rows (>99%), 51 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 617 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1008 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.08, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,338 rows (>99%), 804 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,107 rows (>99%), 1,035 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,028 rows (>99%), 1,114 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,277 rows (>99%), 865 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,101 rows (>99%), 1,041 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,121 rows (>99%), 1,021 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 964 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,511 rows (>99%), 631 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,557 rows (>99%), 585 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,779 rows (>99%), 363 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,440 rows (>99%), 702 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,378 rows (>99%), 764 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,315 rows (99%), 1,827 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 4 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,370 rows (>99%), 772 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,981 rows (99%), 2,161 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,457 rows (>99%), 685 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,762 rows (>99%), 380 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,203 rows (99%), 1,939 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,956 rows (>99%), 186 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,663 rows (>99%), 479 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 390 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.73, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,304 rows (>99%), 838 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,271 rows (>99%), 871 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,497 rows (>99%), 645 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.73, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,931 rows (>99%), 211 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,146 rows (>99%), 996 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,609 rows (>99%), 533 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 123 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,471 rows (>99%), 671 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 29 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,381 rows (>99%), 761 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,613 rows (>99%), 529 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 10 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1490 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.74, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,652 rows (>99%), 490 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,524 rows (>99%), 618 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,122 rows (>99%), 1,020 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,649 rows (>99%), 493 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 114 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,594 rows (>99%), 548 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,577 rows (>99%), 565 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,816 rows (>99%), 326 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,731 rows (>99%), 411 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,708 rows (>99%), 1,434 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,427 rows (>99%), 715 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,469 rows (>99%), 673 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,127 rows (>99%), 1,015 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,129 rows (99%), 2,013 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,499 rows (>99%), 643 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.75, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,686 rows (>99%), 456 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,127 rows (99%), 2,015 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,221 rows (>99%), 921 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 46 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,462 rows (>99%), 1,680 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.05, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,400 rows (>99%), 742 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,849 rows (>99%), 1,293 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,545 rows (>99%), 597 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 360,991 rows (99%), 2,151 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,453 rows (>99%), 689 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,543 rows (>99%), 599 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,607 rows (>99%), 535 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.7, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,590 rows (>99%), 1,552 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,083 rows (>99%), 59 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.36, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,363 rows (>99%), 779 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,025 rows (>99%), 117 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,240 rows (>99%), 902 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1512 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,739 rows (>99%), 403 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,481 rows (>99%), 661 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.81, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,080 rows (>99%), 1,062 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,367 rows (>99%), 775 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,660 rows (>99%), 482 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,157 rows (>99%), 985 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.12, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,767 rows (>99%), 1,375 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,364 rows (>99%), 778 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,994 rows (>99%), 1,148 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.06, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,892 rows (>99%), 250 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.73, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,809 rows (>99%), 1,333 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,480 rows (>99%), 1,662 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,899 rows (>99%), 243 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,529 rows (>99%), 613 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,089 rows (>99%), 1,053 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,198 rows (>99%), 944 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.86, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,689 rows (>99%), 453 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,062 rows (>99%), 80 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 90 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 769 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,144 rows (>99%), 998 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,200 rows (99%), 1,942 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,453 rows (>99%), 689 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 15 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,493 rows (>99%), 649 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 5 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,543 rows (>99%), 599 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 18 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,752 rows (>99%), 390 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 21 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,356 rows (>99%), 786 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 161 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 3 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,961 rows (>99%), 181 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,957 rows (>99%), 185 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 6 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1479 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,625 rows (>99%), 1,517 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,507 rows (>99%), 1,635 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,998 rows (>99%), 144 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 962 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 468 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.78, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,151 rows (>99%), 991 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,081 rows (>99%), 1,061 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,052 rows (>99%), 1,090 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,099 rows (>99%), 1,043 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,630 rows (>99%), 512 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,795 rows (>99%), 1,347 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.34, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,149 rows (99%), 1,993 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,817 rows (>99%), 325 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,721 rows (>99%), 421 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,748 rows (>99%), 394 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,017 rows (>99%), 1,125 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,277 rows (>99%), 865 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3000 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,032 rows (>99%), 110 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 3 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,011 rows (>99%), 131 rows remaining
#> Compiling Stan program...
#> recompiling to avoid crashing R session
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,024 rows (>99%), 118 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 6 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,124 rows (>99%), 18 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 319 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,668 rows (>99%), 474 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,877 rows (>99%), 265 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,022 rows (>99%), 120 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 36 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,073 rows (>99%), 69 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,908 rows (>99%), 234 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1498 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.3, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,881 rows (>99%), 261 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,522 rows (>99%), 620 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,017 rows (>99%), 125 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 437 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 381 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,786 rows (>99%), 356 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,608 rows (>99%), 534 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,088 rows (>99%), 54 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 12 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,761 rows (>99%), 381 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 357 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 3.03, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,486 rows (>99%), 656 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,365 rows (>99%), 777 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,044 rows (>99%), 98 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,096 rows (>99%), 46 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 177 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1663 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.36, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,529 rows (>99%), 613 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,247 rows (>99%), 895 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,079 rows (>99%), 63 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,944 rows (>99%), 198 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,612 rows (>99%), 530 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,377 rows (>99%), 765 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,403 rows (>99%), 739 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,692 rows (>99%), 450 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,982 rows (>99%), 160 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.38, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,993 rows (>99%), 149 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,724 rows (>99%), 418 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,650 rows (>99%), 492 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,968 rows (>99%), 174 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,079 rows (>99%), 63 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 18 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,572 rows (>99%), 570 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,203 rows (>99%), 939 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.7, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,311 rows (>99%), 831 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,314 rows (>99%), 828 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,117 rows (>99%), 1,025 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.8, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,588 rows (>99%), 554 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,214 rows (>99%), 928 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.7, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,596 rows (>99%), 546 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,858 rows (>99%), 284 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,377 rows (>99%), 765 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,881 rows (>99%), 261 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 37 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,996 rows (>99%), 146 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 844 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 2 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.23, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,921 rows (>99%), 221 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2655 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,962 rows (>99%), 180 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 189 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 2 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,818 rows (>99%), 324 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,469 rows (>99%), 673 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,464 rows (>99%), 678 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,921 rows (>99%), 221 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,728 rows (>99%), 414 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,052 rows (>99%), 90 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,985 rows (>99%), 157 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,881 rows (>99%), 261 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 394 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.91, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,795 rows (>99%), 347 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,669 rows (>99%), 473 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,849 rows (>99%), 293 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,920 rows (>99%), 222 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 386 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.92, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,871 rows (>99%), 271 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,883 rows (>99%), 259 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 398 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.92, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,800 rows (>99%), 342 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 12 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,679 rows (>99%), 463 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 231 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,900 rows (>99%), 242 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,699 rows (>99%), 443 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,644 rows (>99%), 498 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 2328 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,994 rows (>99%), 148 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,021 rows (>99%), 121 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,032 rows (>99%), 110 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 29 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,543 rows (>99%), 599 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 40 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1460 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.1, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,429 rows (>99%), 713 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,401 rows (>99%), 741 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.74, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,761 rows (>99%), 381 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,465 rows (>99%), 677 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,170 rows (>99%), 972 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,407 rows (>99%), 735 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.36, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,812 rows (>99%), 330 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,937 rows (>99%), 205 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,054 rows (>99%), 88 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 8 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,408 rows (>99%), 734 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,971 rows (>99%), 171 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,260 rows (>99%), 882 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2717 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,053 rows (>99%), 1,089 rows remaining
#> Compiling Stan program...
#> Start sampling
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,731 rows (>99%), 411 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,810 rows (>99%), 332 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,893 rows (>99%), 249 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,007 rows (>99%), 1,135 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.38, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,209 rows (>99%), 933 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1507 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,753 rows (>99%), 389 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,592 rows (>99%), 550 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,796 rows (>99%), 346 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,464 rows (>99%), 678 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1488 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,704 rows (>99%), 438 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,780 rows (>99%), 362 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,486 rows (>99%), 656 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,392 rows (>99%), 750 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,040 rows (>99%), 102 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 4 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,509 rows (>99%), 633 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,083 rows (>99%), 59 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 84 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1 chains where the estimated Bayesian Fraction of Missing Information was low. See
#> http://mc-stan.org/misc/warnings.html#bfmi-low
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.34, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,547 rows (>99%), 595 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,428 rows (>99%), 714 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,463 rows (>99%), 679 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,704 rows (>99%), 438 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 2.35, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,776 rows (>99%), 366 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,056 rows (>99%), 86 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 9 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,906 rows (>99%), 236 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,794 rows (>99%), 348 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,735 rows (>99%), 407 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.05, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,576 rows (>99%), 566 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 18 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,990 rows (>99%), 152 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 2 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,811 rows (>99%), 331 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,614 rows (>99%), 528 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,833 rows (>99%), 309 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,769 rows (>99%), 373 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,771 rows (>99%), 371 rows remaining
#> Compiling Stan program...
#> recompiling to avoid crashing R session
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,498 rows (>99%), 644 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,435 rows (>99%), 707 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.16, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,878 rows (>99%), 264 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,507 rows (>99%), 635 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,674 rows (>99%), 468 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,642 rows (>99%), 500 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,898 rows (>99%), 244 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 4 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.69, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,052 rows (>99%), 90 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 22 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,777 rows (>99%), 365 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 16 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.68, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 363,107 rows (>99%), 35 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 760 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.1, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,994 rows (>99%), 148 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 51 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1375 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,631 rows (>99%), 511 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 15 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,305 rows (>99%), 837 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.72, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,477 rows (>99%), 665 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1500 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.71, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,067 rows (>99%), 1,075 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 22 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,009 rows (>99%), 1,133 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,975 rows (>99%), 1,167 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 1 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 361,722 rows (>99%), 1,420 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.06, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,603 rows (>99%), 539 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.66, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,842 rows (>99%), 300 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 157 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,904 rows (>99%), 238 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 15 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,673 rows (>99%), 469 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: There were 367 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 202 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 1.73, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,960 rows (>99%), 182 rows remaining
#> Compiling Stan program...
#> Trying to compile a simple C file
#> Running /Library/Frameworks/R.framework/Resources/bin/R CMD SHLIB foo.c
#> clang -mmacosx-version-min=10.13 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I"/Users/maxlindmark/Library/R/4.0/library/Rcpp/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/unsupported" -I"/Users/maxlindmark/Library/R/4.0/library/BH/include" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/src/" -I"/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/" -I"/Users/maxlindmark/Library/R/4.0/library/RcppParallel/include/" -I"/Users/maxlindmark/Library/R/4.0/library/rstan/include" -DEIGEN_NO_DEBUG -DBOOST_DISABLE_ASSERTS -DBOOST_PENDING_INTEGER_LOG2_HPP -DSTAN_THREADS -DBOOST_NO_AUTO_PTR -include '/Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp' -D_REENTRANT -DRCPP_PARALLEL_USE_TBB=1 -I/usr/local/include -fPIC -Wall -g -O2 -c foo.c -o foo.o
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:88:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:1: error: unknown type name 'namespace'
#> namespace Eigen {
#> ^
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/src/Core/util/Macros.h:628:16: error: expected ';' after top level declarator
#> namespace Eigen {
#> ^
#> ;
#> In file included from <built-in>:1:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/StanHeaders/include/stan/math/prim/mat/fun/Eigen.hpp:13:
#> In file included from /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Dense:1:
#> /Users/maxlindmark/Library/R/4.0/library/RcppEigen/include/Eigen/Core:96:10: fatal error: 'complex' file not found
#> #include <complex>
#> ^~~~~~~~~
#> 3 errors generated.
#> make: *** [foo.o] Error 1
#> Start sampling
#> Warning: There were 31 divergent transitions after warmup. See
#> http://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup
#> to find out why this is a problem and how to eliminate them.
#> Warning: There were 1387 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
#> http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
#> Warning: Examine the pairs() plot to diagnose sampling problems
#> Warning: The largest R-hat is 2.37, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,026 rows (>99%), 1,116 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
#> filter: removed 362,204 rows (>99%), 938 rows remaining
#> Compiling Stan program...
#> Start sampling
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> summarise: now one row and 10 columns, ungrouped
#> mutate: new variable 'max_rhat' (double) with one unique value and 0% NA
preds <- map_df(quant_list, ~as.data.frame(.x), .id = "id")
preds <- preds %>%
separate(id, c("area", "cohort"), -5) %>%
mutate(cohort = as.numeric(str_remove(cohort, "_")))
#> mutate: converted 'cohort' from character to double (0 new NA)
ggplot(preds, aes(max_rhat)) +
geom_histogram()
#> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
# Filter "unfit" models
preds <- preds %>% filter(max_rhat < 1.2)
#> filter: removed 337 rows (74%), 120 rows remaining
glimpse(preds)
#> Rows: 120
#> Columns: 13
#> $ area <chr> "BT", "BT", "BT", "BT", "BT", "BT", "BT", "BT", "BT", "BT", "…
#> $ cohort <dbl> 1972, 1973, 1974, 1975, 1978, 1980, 1981, 1984, 1988, 1990, 1…
#> $ K_01 <dbl> 0.16181606, 0.18185407, 0.13261563, 0.04766381, 0.05226494, 0…
#> $ K_025 <dbl> 0.16790837, 0.18682294, 0.13737003, 0.05009596, 0.05559164, 0…
#> $ K_05 <dbl> 0.17471810, 0.19210747, 0.14234104, 0.05275167, 0.05977146, 0…
#> $ K_075 <dbl> 0.18178978, 0.19768087, 0.14739535, 0.05550618, 0.06415369, 0…
#> $ K_09 <dbl> 0.18782354, 0.20247908, 0.15199630, 0.05802888, 0.06858464, 0…
#> $ Linf_01 <dbl> 32.27697, 30.95910, 34.96288, 68.63983, 71.75081, 50.86882, 4…
#> $ Linf_025 <dbl> 32.85155, 31.39573, 35.65861, 71.14135, 75.84969, 52.95792, 4…
#> $ Linf_05 <dbl> 33.58896, 31.91775, 36.49526, 74.24880, 80.63988, 55.44892, 4…
#> $ Linf_075 <dbl> 34.39011, 32.42892, 37.37056, 77.53232, 85.75492, 58.21454, 4…
#> $ Linf_09 <dbl> 35.13746, 32.93959, 38.24982, 80.87107, 90.59189, 61.07799, 4…
#> $ max_rhat <dbl> 1.005, 1.021, 1.082, 1.004, 1.016, 1.007, 1.010, 1.048, 1.020…
# K
ggplot(preds, aes(cohort, K_05, color = area)) +
geom_line()
ggplot(preds, aes(cohort, K_05, color = area)) +
geom_line() +
facet_wrap(~area)
# preds %>%
# filter(area == "BT") %>%
# ggplot(aes(cohort, K_05)) +
# geom_ribbon(aes(ymin = K_01, ymax = K_09), fill = "grey80") +
# geom_line()
#
# preds %>%
# filter(area == "BT") %>%
# ggplot(aes(cohort, K_05)) +
# geom_errorbar(aes(ymin = K_01, ymax = K_09), fill = "grey80") +
# geom_point()
#
# ggplot(preds, aes(cohort, K_05)) +
# geom_ribbon(aes(ymin = K_01, ymax = K_09), fill = "grey20") +
# geom_line() +
# facet_wrap(~area)
# L_inf
ggplot(preds, aes(cohort, Linf_05, color = area)) +
geom_line()
ggplot(preds, aes(cohort, Linf_05, color = area)) +
geom_line() +
facet_wrap(~area)
preds %>% filter(max_rhat > 4)
#> filter: removed all rows (100%)
# BT 1971 looks problematic
dd <- filter(d, area == "BT", cohort == 1971)
#> filter: removed 363,047 rows (>99%), 95 rows remaining
ggplot(dd, aes(age_bc, length_cm, color = ID)) +
geom_point() +
geom_line() +
scale_color_viridis(discrete = TRUE)
m <-
brm(
bf(length_cm ~ Linf*(1-exp(-K*(age_bc-t0))),
t0 ~ 1,
K ~ 1 + (1|ID),
Linf ~ 1,
nl = TRUE),
data = dd,
family = gaussian(),
prior = c(prior(normal(45, 20), nlpar = "Linf"),
prior(normal(-0.5, 1), nlpar = "t0"),
prior(normal(0.2, 0.1), nlpar = "K")),
iter = 3000,
thin = 1,
cores = 3,
chains = 3,
seed = 9)
#> Compiling Stan program...
#> Start sampling
#> Warning: The largest R-hat is 1.67, indicating chains have not mixed.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#r-hat
#> Warning: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#bulk-ess
#> Warning: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
#> Running the chains for more iterations may help. See
#> http://mc-stan.org/misc/warnings.html#tail-ess
rhat(m)
#> b_t0_Intercept b_K_Intercept
#> 6.299701 6.379637
#> b_Linf_Intercept sd_ID__K_Intercept
#> 7.084453 1.983392
#> sigma r_ID__K[1977_123_BT,Intercept]
#> 3.025837 2.002740
#> r_ID__K[1977_145_BT,Intercept] r_ID__K[1977_152_BT,Intercept]
#> 1.064385 1.191307
#> r_ID__K[1977_90_BT,Intercept] r_ID__K[1977_98_BT,Intercept]
#> 1.826052 1.696548
#> r_ID__K[1978_152_BT,Intercept] r_ID__K[1978_153_BT,Intercept]
#> 2.270501 1.021973
#> r_ID__K[1978_155_BT,Intercept] r_ID__K[1978_248_BT,Intercept]
#> 1.741322 1.010553
#> r_ID__K[1978_313_BT,Intercept] r_ID__K[1978_53_BT,Intercept]
#> 1.339868 1.000945
#> r_ID__K[1978_83_BT,Intercept] r_ID__K[1979_129_BT,Intercept]
#> 1.706484 1.205390
#> r_ID__K[1979_144_BT,Intercept] lprior
#> 1.983721 7.116406
#> lp__
#> 6.719984
summary(m)
#> Warning: Parts of the model have not converged (some Rhats are > 1.05). Be
#> careful when analysing the results! We recommend running more iterations and/or
#> setting stronger priors.
#> Family: gaussian
#> Links: mu = identity; sigma = identity
#> Formula: length_cm ~ Linf * (1 - exp(-K * (age_bc - t0)))
#> t0 ~ 1
#> K ~ 1 + (1 | ID)
#> Linf ~ 1
#> Data: dd (Number of observations: 95)
#> Draws: 3 chains, each with iter = 3000; warmup = 1500; thin = 1;
#> total post-warmup draws = 4500
#>
#> Group-Level Effects:
#> ~ID (Number of levels: 14)
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> sd(K_Intercept) 0.01 0.01 0.00 0.03 1.67 5 33
#>
#> Population-Level Effects:
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> t0_Intercept -0.80 0.97 -2.55 0.06 1.66 5 35
#> K_Intercept 0.09 0.10 -0.06 0.20 1.66 5 35
#> Linf_Intercept 9.64 39.59 -60.64 42.28 1.66 5 44
#>
#> Family Specific Parameters:
#> Estimate Est.Error l-95% CI u-95% CI Rhat Bulk_ESS Tail_ESS
#> sigma 1.27 0.30 0.94 1.87 1.66 5 35
#>
#> Draws were sampled using sampling(NUTS). For each parameter, Bulk_ESS
#> and Tail_ESS are effective sample size measures, and Rhat is the potential
#> scale reduction factor on split chains (at convergence, Rhat = 1).
plot(m)